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Comparative Genomics

General resources for comparison of sequences and genomes.

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Found 39 links

Displaying 15 links

agriGOTool Content

http://bioinfo.cau.edu.cn/agriGO/

DNA > Annotations
Model Organisms > Plants
Sequence Comparison > Comparative Genomics

agriGO is an integrated gene ontology analysis toolkit for the agriculture community. Supported organisms and gene identifiers were expanded over EasyGO tool, and several tools for predicting gene function are included.

NAR Web Server Issue 2010
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tagsagricultural crops plant genes

ATIVSTool Content

http://influenza.nhri.org.tw/ATIVS/

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

ATIVS (analytical tool for influenza virus surveillance) is a web server for analyzing serological data of all influenza viruses and provide interpretive summaries. ATIVS also compares the HA1 sequences of viruses to those of the reference vaccine strains to predict influenza A/H3N2 antigenic drift.

This content is being maintained by Jade.

NAR Web Server Issue 2009
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tagsantigenic variation h3n2 subtype influenza a virus human influenza humans influenza virus hemagglutinin glycoproteins orthomyxoviridae population surveillance sequence analysis viral antibodies viral antigens

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

CGView ServerTool Content

http://stothard.afns.ualberta.ca/cgview_server/

DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots. The server uses BLAST to compare the primary sequence of up to three genomes or sequence sets, aiding in the identification of conserved genome segments, instances of horizontal transfer or visualization of genome segments from newly obtained sequence reads.

This content is being maintained by jason.grant.

NAR Web Server Issue 2008
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tagsbacterial genome chloroplast genome chromosome mapping circular dna genomics mitochondrial genome plasmids sequence alignment

CisMolsTool Content

http://cismols.cchmc.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Sequence Comparison > Comparative Genomics

CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.

NAR Web Server Issue 2005
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tagsbase sequence binding sites conserved sequence gene expression regulation genomics response elements transcription factors

CMRDatabase Content

http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

The Comprehensive Microbial Resource (CMR) gives access to a central repository of the sequence and annotation of all complete public prokaryotic genomes as well as comparative genomics tools across all of the genomes in the database.

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tagsbacteria bacterial genes bacterial genome factual databases information services

COGsTool Content

http://www.ncbi.nlm.nih.gov/COG/

Protein > Domains and Motifs
Sequence Comparison > Comparative Genomics

Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.

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tagsamino acid sequence animals archaea archaeal genes archaeal proteins bacteria bacterial genes bacterial proteins caenorhabditis elegans conserved sequence drosophila melanogaster factual databases fungal genes fungal proteins genome methanococcus molecular evolution multigene family phylogeny proteins saccharomyces cerevisiae sequence alignment species specificity

CoMetTool Content

http://comet.gobics.de

Sequence Comparison > Comparative Genomics

CoMet is a web server for comparative metagenomics, and is particularly suited for analysis of large collections of metagenomic short read data.

NAR Web Server Issue 2011
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DAVID Bioinformatics ResourcesTool Content

http://david.abcc.ncifcrf.gov/home.jsp

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

NAR Web Server Issue 2007
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tagsalgorithms automated pattern recognition computational biology gene expression profiling genetic databases genomics hiv-1 humans macrophages mononuclear leukocytes nucleic acid databases oligonucleotide array sequence analysis statistical data interpretation

DCODE.ORGResource Content

http://www.dcode.org/

Human Genome > Other Resources
Sequence Comparison > Comparative Genomics

The dcode.org website provides access to tools for comparative genomic analyses developed by the Comparative Genomics Center at the Lawerence Livermore National Laboratory. Tools include: zPicture, Mulan, eShadow, rVista, CREME, and the ECR Browser.

NAR Web Server Issue 2005
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tagsbase sequence binding sites computational biology gene expression regulation genetic promoter regions genomics humans molecular evolution nucleic acid regulatory sequences phylogeny sequence alignment transcription factors

EnteriXTool Content

http://enterix.cbcb.umd.edu/

Model Organisms > Microbes
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.

NAR Web Server Issue 2003
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tagsbacterial dna bacterial genome conserved sequence dna sequence analysis enterobacteriaceae escherichia coli gene components gene deletion genomics nucleic acid regulatory sequences nucleotidyltransferases salmonella sequence alignment

G-SESAMETool Content

http://bioinformatics.clemson.edu/G-SESAME

Expression > Gene Set Analysis
Literature > Text Mining and Semantics
Sequence Comparison > Comparative Genomics

G-SESAME is a suite of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, as well as data mining the GO database.

NAR Web Server Issue 2009
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tagscluster analysis controlled vocabulary genes genetic databases

GeConT 2Tool Content

http://gecont.ibt.unam.mx/cgi-bin/gecont/gecont.pl

DNA > Sequence Retrieval and Submission
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

The Gene Context Tool (GeConT) is a visualization tool for viewing the genomic context of a gene or group of genes, and their orthologous relationships, within any of the fully sequenced bacterial genomes. Sequence retrieval is also possible.

NAR Web Server Issue 2008
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tagsbacteria bacterial genes bacterial genome bacterial proteins conserved sequence genomics tertiary protein structure

GenomeTraFaCTool Content

http://genometrafac.cchmc.org/genome-trafac/index.jsp

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

GenomeTraFaC is a comparative genomics based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq gene orthologs.

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tagsanimals base sequence binding sites conserved sequence genomics humans mice micrornas nucleic acid databases transcription factors transcriptional regulatory elements

InsigniaTool Content

http://insignia.cbcb.umd.edu

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

Insignia provides a web interface for identifying unique genomic signatures from a database of all current bacterial and viral genomic sequences. Input is any set of target and background genomes.

NAR Web Server Issue 2009
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tagsanimals bacteria bacterial genome dna sequence analysis humans infection viral genome viruses

Tags associated with subcategory 'Sequence Comparison/Comparative Genomics'

genomics humans animals bacterial genome sequence alignment phylogeny computational biology dna sequence analysis algorithms conserved sequence genetic databases nucleic acid databases molecular evolution mice genome base sequence proteins nucleic acid sequence homology binding sites bacterial genes nucleic acid regulatory sequences molecular sequence data gene expression profiling transcription factors amino acid sequence homology plant dna helminth genes horizontal gene transfer introns protein biosynthesis parasites plant genome nematoda oligonucleotides metabotropic glutamate receptors bacterial meningitis bacterial typing techniques cerebrospinal fluid evaluation studies as topic cluster analysis spirurida software design dna primers rna editing genetic predisposition to disease neoplasm proteins tissue distribution protein isoforms caenorhabditis elegans proteins helminth dna enterobacteriaceae escherichia coli escherichia coli o157 genetic recombination gene rearrangement computer simulation bacterial dna genetic promoter regions dna-binding proteins intestines lung untranslated rna organ specificity salmonella typhi salmonella typhimurium database management systems codon drosophila drosophila proteins genetic variation expressed sequence tags gene frequency caenorhabditis elegans software validation shigella flexneri theoretical models xeroderma pigmentosum group d protein benchmarking base composition response elements meningococcal infections chromosome mapping dna dogs human chromosomes exons chickens cattle protein sequence analysis multigene family saccharomyces cerevisiae cats species specificity human genome kinesin single nucleotide polymorphism swine takifugu untranslated regions time factors sensitivity and specificity